Torsional motion, molecular

Terms in the energy expression that describe a single aspect of the molecular shape, such as bond stretching, angle bending, ring inversion, or torsional motion, are called valence terms. All force fields have at least one valence term and most have three or more. 

When the friction coefficient is set to zero, HyperChem performs regular molecular dynamics, and one should use a time step that is appropriate for a molecular dynamics run. With larger values of the friction coefficient, larger time steps can be used. This is because the solution to the Langevin equation in effect separates the motions of the atoms into two time scales the short-time (fast) motions, like bond stretches, which are approximated, and longtime (slow) motions, such as torsional motions, which are accurately evaluated. As one increases the friction coefficient, the short-time motions become more approximate, and thus it is less important to have a small timestep. 

If one rotates about a C-C single bond in a compound of type X-C-C-Y, at each step of this torsional motion there are electron redistributions, and the bond lengths and angles will change. This phenomenon is the basis of the local nature of molecular structure. Several examples are illustrated in Figs. 7.6 and 7.7. 

If it is desired to know how certain molecular properties of the solute (e.g., conformations) are affected by the presence of the solvent, then it is necessary to augment Eqs. (16) and (17) by appropriate solute intramolecular potentials. These would account for stretching, bending and torsional motions, plus any others deemed significant for typical formulations, see Kollman,10 Maple,61 and Politzer and Boyd.67 Equations (16) and (17) would also be expanded to encompass solute intramolecular interactions. 

Empirical force fields used in molecular mechanics/molecular dynamics calculations all share common components, among them components which describe bond-stretching, angle-bending and torsional motions, as well as components which account for non-bonded steric and electrostatic interactions. While much of the information needed to parameterize force fields can be obtained from experiment, quite frequently critical data are missing. Information about torsional potentials, in particular, is often very difRcult to obtain from experiment, and here calculations can prove of great value. 

The partition function of a molecule also contains torsional motions and the construction of such a function requires the knowledge of molecular mass, moments of inertia, and constants describing normal vibration modes. Several of these data may be acquired from infrared and Raman spectra (67SA(A)891 85JST( 126)25), but the procedure has not yet been extensively applied owing to experimental limitations. To characterize the barrier one also needs to know more than one constant, and these are often not available from... 

The choice of series is not only dependent on the type of molecular motion. For example the power series may be convenient for an accurate description of the potential function close to the minima, while a Fourier series is convenient for describing potential barriers to torsional motion. 

As discussed in the introduction to this chapter the final rotation of the photofragment reflects three sources overall rotation of the parent molecule, which is preserved in the electronic excitation process, internal bending or torsional motion in the electronic ground state, and final state interaction. The latter two sources have been analyzed in Sections 10.1-10.4. The influence of overall rotation will be discussed in this section. Its relative contribution increases gradually with the magnitude of the total angular momentum J and therefore it increases with the temperature of the molecular sample. As we will demonstrate below, the conversion of overall rotation of the parent molecule in the electronic ground state into... 

In the amorphous regions of PTFE we identify d with the time average of the local chain direction and with its instantaneous direction. Since the torsional motion about the chain axis above -68°C is such that we retain effective axial symmetry of the chemical shift with respect to the molecular chain axis, we do have the angular dependence required by condition (i) ... 

Classical interaction potentials for molecular systems can be pairwise or take manybody interactions into account, molecules can be rigid or flexible, and both stretching and torsion motions can be considered [28]. Polarizability can be introduced, but for example for water this does not seem to make the potentials mimic reality unambiguously better. The potentials, also called force fields, are fitted to reproduce certain sets of properties, and can fail to reproduce other characteristics. The potentials suffer from problems with transferability for example a water-sulfuric acid potential developed for the two-component mixture does not necessarily describe the interaction between water and sulfuric acid in a three-component mixture of water, sulfuric acid and ammonia. Also, potentials created for bulk liquid do not always work for surface layers or small clusters. 

Aromatic sulfides analogous to thiophenols constitute a group of molecules that fulfils the structural conditions necessary for the observation of FET (Sec. 2.4), i.e. they exhibit a low barrier to rotation about the Qp2 S bond. Thus, the torsion motions of the substituents can be accompanied by considerable fluctuation of the electrons in the highest molecular orbitals with two extreme examples of conformers, planar and vertical. The presence of two radical cation conformers was deduced as primary products of the bimolecular free electron transfer (FET) from aromatic sulfides PhSCH2Ph, PhSCHPhj, and PhSCPhg to w-butyl chloride radical based on the nanosecond pulse radiolysis experiments. ... 

In the last part of this chapter, intramolecular charge transfer (ICT) in anthryl derivatives with linked donor-acceptor parts was discussed. Ultrafast spectroscopy has been applied both for structural characterization and for real-time probing of the ICT in this case. Microscopic solvation effects on the torsional motions and the ICT in the molecules have been examined by the use of their clusters with polar solvents. One of the most important problems which awaits for further studies is an ambiguous description of the electronic character of the charge-separated states in the systems. So far, high-level quantum-mechanical calculations have not been able to deal with such large molecular systems, but reliable evaluation of electronically... 

K. P. Travis, D. Brown and J. H. R. Clarke, A Molecular Dynamics Study of the Coupling of Torsional Motions to Self-Diffusion in Liquid Hexane J. Chem. Phys. 102(1995)2174-2180. 

This character results from quinonoid resonance structures in addition to the more important Kekul6-type structures and tends to cause the hydrogen atom to be placed in the molecular plane. This leads to two equivalent configurations with the hydrogen of the OH group being on one side of the other of the C—O bond . It implies the existence of the activation barrier K of the OH torsion motion around the C—O bond estimated in the mid-thirties as equal to 14 kJmoU . 

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